In the previous study, a new method was established to prepare mannan under mild conditions by using antibiotic Benanomicin A. In this study, this method was applied to the isolation of P. pastoris NBRC 0984 mannan which predominantly contains β-1,2-linked mannose residues. As the findings of nuclear magnetic resonance (NMR) analysis of the resultant mannan to examine the distribution state of the side chain, it was found that despite the existence of oligomannosyl side chains corresponding to pentaose, Manα1→2Manβ1→Manβ1→Manα1→2Man, tetraose, Manβ1→Manβ1→Manα1→2Man, and biose, Manα1→2Man, in this molecule, the side chain corresponding to triose, Manβ1→Manα1→2Man, was not detected at all. In our previous study, a relatively large number of biosyl and triosyl side chains were detected in analyzes applying acetolysis to mannans prepared by the Fehling method from the same yeast cells. Such a difference can be explained as that the β-1,2-linkages of some pentaosyl and tetraosyl side chains were cleaved by acetolysis, and triose and biose occurred secondarily in large quantities. In conclusion, the best way to accurately measure the side chain distribution of mannan is to perform NMR analysis on untreated mannan molecules prepared under mild conditions using Benanomicin A.